User:Shal613/Quantum biology

Can't believe that I didn't publish the changes that I had made originally...

''First order of business is to restructure the article so that it has increased readability. Added the following sentence to the introduction and reorganized the entire article to revolve around this statement.''

Currently, there exist four major life processes that have been identified as influenced by quantum effects: enzyme catalysis, sensory processes , energy transference , and information encoding.

Notes to self

Light reactions

Photons converted to energy (ATP, NADPH)

Calvin Cycle

Uses energy to build G3P, precursor to glucose

Chloroplast -> Thylakoids (Stacked as Granum).

Chlorophyll is part of membrane bound proteins in the thylakoids

Photosystem

Chlorophylls make up photosystems (excitation and photon passing between chlorophyl)

Photon passed to reaction center complex, which transfers electron to primary electron acceptor. Later, this missing electron is enzymatically taken from water

Photosystem II converts photon energy into free electron. Electron then passed to plastoquinone, cytochrome and then Photosystem I. NADP is the final electron acceptor. This passing pumps H+ inside the thylakoid lumen to then power ATP synthase

Photosynthesis
Photosynthesis refers to the biological process that photosynthetic cells use to synthesize organic compounds from inorganic starting materials using sunlight. What has been primarily implicated as reflecting non-trivial quantum behaviors is the light reaction stage of photosynthesis. In this stage, photons are absorbed by the membrane-bound photosystems. Photosystems contain two major domains, the light harvesting complex (antennae) and the reaction center. These antennae vary among organisms. For example, bacteria use circular aggregates of chlorophyll pigments, while plants use membrane-embedded protein and chlorophyll complexes. Regardless, photons are first captured by the antennae and passed on to the reaction center complex. Various pigment-protein complexes, such as the FMO complex in green sulfur bacteria, are responsible for transferring energy from antennae to reaction site. The photon driven excitation of the reaction center complex mediates its oxidation and the reduction the primary electron acceptor, a component of the reaction center complex. Much like the electron transport chain of the mitochondria, a linear series of oxidations and reductions drives proton (H+) pumping across the thylakoid membrane, the development of a proton motive force, and energetic coupling to the synthesis of ATP.

Previous understandings of electron excitation transference (EET) from light-harvesting antennae to the reaction center have relied on the Förster theory of incoherent EET, postulating weak electron coupling between chromophores and incoherent hopping from one to another. This theory has largely been disproven by FT electron spectroscopy experiments that show electron absorption and transfer show an efficiency of above 99%, which cannot be explained by classical mechanical models. Instead, as early as 1938, scientists theorized that quantum coherence was the mechanism for excitation energy transfer. Indeed, the structure and nature of the photosystem places it in the quantum realm, with EET ranging from the femto to nanosecond scale, covering sub-nanometer to nanometer distances. The effects of quantum coherence on EET in photosynthesis are best understoood through state and process coherence. State coherence refers to the extent of individual superpositions of ground and excited states for quantum entities, such as excitons. Process coherence, on the other hand, refers to degree of coupling between multiple quantum entities and their evolution as either dominated by unitary or dissipative parts, which compete with one another. Both these types of coherences are implicated in photosynthetic EET, where a exciton is coherently delocalized over several chromophores. This delocalization allows for the system to simultaneously explore several energy paths and use constructive and destructive interference to guide the path of the exciton's wave packet. It is presumed that natural selection has favored the most efficient path to the reaction center. Experimentally, the interaction between the different frequency wave packets, made possible by long-lived coherence, will produce quantum beats.

While quantum photosynthesis is still an emerging field, there have been many experimental results that support the quantum coherence understanding of photosynthetic EET. A 2007 study claimed the identification of electronic quantum coherence at −196 °C (77 K). Another theoretical study from 2010 provided evidence that quantum coherence lives as long as 300 femtoseconds at biologically relevant temperatures (4 °C or 277 K). In that same year, experiments conducted on photosynthetic cryptophyte algae using two-dimensional photon echo spectroscopy yielded further confirmation for long-term quantum coherence. These studies suggest that, through evolution, nature has developed a way of protecting quantum coherence to enhance the efficiency of photosynthesis. However, critical follow-up studies question the interpretation of these results. Single molecule spectroscopy now shows the quantum characteristics of photosynthesis without the interference of static disorder, and some studies use this method to assign reported signatures of electronic quantum coherence to nuclear dynamics occurring in chromophores. A number of proposals emerged to explain unexpectedly long coherence. According to one proposal, if each site within the complex feels its own environmental noise, the electron will not remain in any local minimum due to both quantum coherence and thermal environment, but proceed to the reaction site via quantum walks. Another proposal is that the rate of quantum coherence and electron tunneling create an energy sink that moves the electron to the reaction site quickly. Other work suggested that geometric symmetries in the complex may favor efficient energy transfer to the reaction center, mirroring perfect state transfer in quantum networks. Furthermore, experiments with artificial dye molecules cast doubts on the interpretation that quantum effects last any longer than one hundred femtoseconds.

In 2017, the first control experiment with the original FMO protein under ambient conditions confirmed that electronic quantum effects are washed out within 60 femtoseconds, while the overall exciton transfer takes a time on the order of a few picoseconds. In 2020 a review based on a wide collection of control experiments and theory concluded that the proposed quantum effects as long lived electronic coherences in the FMO system does not hold. Instead, research investigating transport dynamics suggests that interactions between electronic and vibrational modes of excitation in FMO complexes require a semi-classical, semi-quantum explanation for the transfer of exciton energy. In other words, while quantum coherence dominates in the short-term, a classical description is most accurate to describe long-term behavior of the excitons.

Another process in photosynthesis that has almost 100% efficiency is charge transfer, again suggesting that quantum mechanical phenomena are at play. In 1966, a study on the photosynthetic bacterium Chromatium found that at temperatures below 100 K, cytochrome oxidation is temperature-independent, slow (on the order of milliseconds), and very low in activation energy. The authors, Don DeVault and Britton Chase, postulated that these characteristics of electron transfer are indicative of quantum tunneling, whereby electrons penetrate a potential barrier despite possessing less energy than is classically necessary.

Pigment-protein complexes (PPCs)

Photosynthetic organisms absorb light energy through the process of electron excitement in antennae. These antennae vary among organisms. For example, bacteria use ring-like antennae, while plants use chlorophyll pigments to absorb photons. Photosynthesis creates Frenkel excitons, which provide a separation of charge that cells convert into usable chemical energy. The energy collected in reaction sites must be transferred quickly before it is lost to fluorescence or thermal vibrational motion.

Various structures, such as the FMO complex in green sulfur bacteria, are responsible for transferring energy from antennae to a reaction site. FT electron spectroscopy studies of electron absorption and transfer show an efficiency of above 99%, which cannot be explained by classical mechanical models like the diffusion model. Instead, as early as 1938, scientists theorized that quantum coherence was the mechanism for excitation energy transfer.

Scientists have looked for experimental evidence of this proposed energy transfer mechanism. A 2007 study claimed the identification of electronic quantum coherence at −196 °C (77 K). Another theoretical study from 2010 provided evidence that quantum coherence lives as long as 300 femtoseconds at biologically relevant temperatures (4 °C or 277 K). In that same year, experiments conducted on photosynthetic cryptophyte algae using two-dimensional photon echo spectroscopy yielded further confirmation for long-term quantum coherence. These studies suggest that, through evolution, nature has developed a way of protecting quantum coherence to enhance the efficiency of photosynthesis. However, critical follow-up studies question the interpretation of these results. Single molecule spectroscopy now shows the quantum characteristics of photosynthesis without the interference of static disorder, and some studies use this method to assign reported signatures of electronic quantum coherence to nuclear dynamics occurring in chromophores. A number of proposals emerged to explain unexpectedly long coherence. According to one proposal, if each site within the complex feels its own environmental noise, the electron will not remain in any local minimum due to both quantum coherence and thermal environment, but proceed to the reaction site via quantum walks. Another proposal is that the rate of quantum coherence and electron tunneling create an energy sink that moves the electron to the reaction site quickly. Other work suggested that geometric symmetries in the complex may favor efficient energy transfer to the reaction center, mirroring perfect state transfer in quantum networks. Furthermore, experiments with artificial dye molecules cast doubts on the interpretation that quantum effects last any longer than one hundred femtoseconds.

In 2017, the first control experiment with the original FMO protein under ambient conditions confirmed that electronic quantum effects are washed out within 60 femtoseconds, while the overall exciton transfer takes a time on the order of a few picoseconds. In 2020 a review based on a wide collection of control experiments and theory concluded that the proposed quantum effects as long lived electronic coherences in the FMO system does not hold. Instead, research investigating transport dynamics suggests that interactions between electronic and vibrational modes of excitation in FMO complexes require a semi-classical, semi-quantum explanation for the transfer of exciton energy. In other words, while quantum coherence dominates in the short-term, a classical description is most accurate to describe long-term behavior of the excitons.

Another process in photosynthesis that has almost 100% efficiency is charge transfer, again suggesting that quantum mechanical phenomena are at play. In 1966, a study on the photosynthetic bacterium Chromatium found that at temperatures below 100 K, cytochrome oxidation is temperature-independent, slow (on the order of milliseconds), and very low in activation energy. The authors, Don DeVault and Britton Chase, postulated that these characteristics of electron transfer are indicative of quantum tunneling, whereby electrons penetrate a potential barrier despite possessing less energy than is classically necessary.

Mitochondria
Organelles, such as mitochondria, are thought to utilize quantum tunneling in order to translate intracellular energy. Traditionally, mitochondria are known to generate most of the cell's energy in the form of chemical ATP. Mitochondria conversion of biomass into chemical ATP is 60-70% efficient, which is superior than the classical regime of man-made engines. To achieve chemical ATP, researchers have found that a preliminary stage before chemical conversion is necessary; this step, via the quantum tunneling of electrons and hydrogen ions (H+), requires a deeper look at the quantum physics that occurs within the organelle.

Mitochondria have been demonstrated to utilize quantum tunneling in its function as the powerhouse of eukaryotic cell. Similar to the light reactions in the thylakoid, linearly associated membrane bound proteins comprising the electron transport chain (ETC) energetically link the reduction of O2 with the development of a proton motive gradient (H+) across the inner membrane of the mitochondria. This energy stored as a proton motive gradient is then coupled with the synthesis of ATP. It is significant that the mitochondrion conversion of biomass into chemical ATP achieves 60-70% thermodynamic efficiency, far superior to that of man-made engines. This high degree of efficiency is largely attributed to the quantum tunnelling of electrons in the ETC and of protons in the proton motive gradient. Indeed, quantum electron tunneling has already been demonstrated in certain elements of the ETC including NADH:ubiquinone oxidoreductase (Complex I) and CoQH2-cytochrome c reductase (Complex III).

Because tunneling is a quantum mechanism, it is important to understand how this process may occur for particle transfer in a biological system. In quantum mechanics, both electrons and protons are quantum entities that exhibit wave-particle duality, exhibiting both particle and wave like properties depending on the method of experimental observation. Quantum tunneling is a direct consequence of this wave-like nature of quantum entities that permits the passing-through of a potential energy barrier that would otherwise restrict the entity. Moreover, it depends on the shape and size of a potential barrier, relative to the incoming energy of a particle. Because the incoming particle can be defined by a wave equation its wave function, its tunneling probability is dependent upon the potential barrier's shape in an exponential way. For example, meaning that if the barrier is akin to a very wide chasm relatively wide, the incoming particle's probability to tunnel will decrease. The potential barrier, in some sense, can come in the form of an actual biomaterial barrier. Mitochondria are encompassed by a membrane structure that is akin to the cellular membrane The inner mitochondria membrane which houses the various components of the ETC is on the order of ~75 Å (~7.5 nm) thick. The inner membrane of a mitochondrion must be overcome to permit signals (in the form of electrons, protons, H+) to transfer from the site of emittance (internal to the mitochondria) and the site of acceptance (i.e. the electron transport chain proteins). In order to transfer particles, the membrane of the mitochondria must have the correct density of phospholipids to conduct a relevant charge distribution that attracts the particle in question. For instance, for a greater density of phospholipids, the membrane contributes to a greater conductance of protons.

''Unnecessary to this article. All this information is found in the wiki link to ETC''

More technically, the form of the mitochondria is the matrix, with inner mitochondrial membranes (IMM) and inner membrane spaces (IMS), all housing protein sites. Mitochondria produce ATP by the oxidation of hydrogen ions from carbohydrates and fats. This process utilizes electrons in an electron transport chain (ETP). The genealogy of electron transport proceeds as follows: Electrons from NADH are transferred to NADH dehydrogenase (complex I protein), which is located in the IMM. Electrons from complex I are transferred to coenzyme Q to make CoQH2; next, electrons flow to cytochrome-containing IMM protein (complex III), which further pushes electrons to cytochrome c, where electrons flow to complex IV; complex IV is the final IMM protein complex of the ETC respiratory chain. This final protein allows electrons to reduce oxygen from an O2 molecule to a single O, so that it can bind to the hydrogen ions to produce H2O. The energy produced from the movement of electrons through the ETC induces proton movement (known as H+ pumping) out of the mitochondria matrix into the IMS. Because any charge movement creates a magnetic field, the IMS now houses a capacitance across the matrix. The capacitance is akin to potential energy, or what is known as a potential barrier. This potential energy guides ATP synthesis via complex V (ATP synthase), which conflates ADP with another P to create ATP by pushing protons (H+) back into the matrix (this process is known as oxidative phosphorylation). Finally, the outer mitochondrial membrane (OMM) houses a voltage-dependent anion channel called the VDAC. This site is important for converting energy signals into electro-chemical outputs for ATP transfer.